Pre-processing

Model

[Metric] ~ Group * Measurement + (1|AnimalTrial)

Baseline (intercept): Group = “KIT” & Measurement = “postLaser”

library(tidyverse)
library(ggpubr)
library(rstatix)
library(knitr)
library(kableExtra)
library(nlme)
library(emmeans)
library(standardize)
library(sjPlot)
library(gridExtra)
library(effectsize)
data_type <- "CLST"
raw_data <- read_csv(paste0("../../Data_new/AVRECPeak", data_type,".csv"))

layers <- unique(raw_data$Layer)
metrics <- c("RMS", "logRMS")
stimfreq <- c(5, 10)

# layers <- c("All", "IV")
# metrics <- c("logRMS")
# stimfreq <- c(5)

red_color <- "#ffb3b3"
green_color <- "#d6f5d6"

# values for testing
layer <- "All"
freq <- 5
metric <- "logRMS"
all_data <- raw_data %>% 
  filter(
    OrderofClick == 1, # just 1st click
    grepl('_1', Measurement), # pre/post Laser
    PeakAmp > 0 # remove NAs
  ) %>% 
  mutate(
    Measurement = case_when(
      grepl('pre', Measurement) ~ "preLaser",
      TRUE ~ "postLaser"),
    Measurement = factor(Measurement, levels = c("postLaser", "preLaser")),
    Animal = factor(Animal),
    TrialNumber = factor(TrialNumber),
    Group = factor(Group, levels = c("KIT", "KIC", "KIV")),
    logRMS = log(RMS)
  )

# # combine Animal + TrialNumber into 1 column
# if(grepl("ST", data_type)){
#   model_data <- model_data %>%
#     mutate(Animal = paste0(Animal, "_", TrialNumber)) %>%
#     select(-TrialNumber) %>%
#     ungroup()
# }

# get average by Trial
# if(grepl("ST", data_type)){
#   all_data <- all_data %>%
#     group_by(Group, Animal, Measurement, Layer, ClickFreq) %>%
#     summarize(
#       PeakAmp = mean(PeakAmp, na.rm = TRUE),
#       PeakLat = mean(PeakLat, na.rm = TRUE),
#       RMS = mean(RMS, na.rm = TRUE),
#       logRMS = mean(logRMS, na.rm = TRUE)) %>%
#     ungroup()
# }

Results

for (freq in stimfreq){

    cat("##", freq, "Hz Frequency {.tabset .tabset-fade .tabset-pills} \n")
  
  cat('\n\n')
  
  for(layer in layers){

    cat("###", layer, "Layer {.tabset .tabset-fade .tabset-pills} \n")
    
    model_data <- all_data %>% 
      filter(ClickFreq == freq,
             Layer == layer)
    
    for(metric in metrics){

      cat("####", metric, "{.tabset .tabset-fade .tabset-pills} \n")
      
      cat("##### Data overview\n")
      
      cat('\n\n')
      
      model_data %>% 
        select(-c(OrderofClick, Layer, ClickFreq)) %>% 
        sample_n(5) %>% 
        kable(escape = F, digits = 6,
            caption = "Sample of the data") %>%
        kable_classic_2(full_width = F) %>% 
        kable_styling() %>% 
        print()
      
      cat('\n\n')
      
      # plots with data overview
      box_plot <- ggboxplot(
        model_data, x = "Group", y = metric,
        color = "Measurement", palette = "lancet", 
        add = "jitter",
        main = paste0(metric, " ~ Group | Measurement")
      )
      plot(box_plot)
      
      box_plot2 <- ggboxplot(
        model_data, x = "Measurement", y = metric,
        color = "Group", palette = "jco", 
        add = "jitter",
        main = paste0(metric, " ~ Measurement | Group")
      )
      plot(box_plot2)
      
      cat('\n\n')
      
      # cat("##### Assumption check\n")
      # 
      # cat("<b>===OUTLIERS===</b>\n\n")
      # 
      # df <- model_data %>%
      #   group_by(Measurement, Group) %>%
      #   identify_outliers(eval(metric))
      # 
      # if(nrow(df) > 0){
      #   df %>% 
      #   kable(escape = F, digits = 6,
      #         caption = "Outliers") %>%
      #   kable_classic_2(full_width = F) %>% 
      #   kable_styling() %>% 
      #   row_spec(
      #     which(df$is.extreme == TRUE), bold = T, 
      #     background = red_color) %>% 
      #   print()
      # } else{
      #   cat("\n\nNo outliers were detected.\n\n")
      # }
      # 
      # cat("\n\n<b>===NORMALITY ASSUMPTION===</b>\n\n")
      # 
      # p <- ggqqplot(model_data, metric, ggtheme = theme_bw()) +
      #   facet_grid(Group ~ Measurement, labeller = "label_both")
      # plot(p)
      # 
      # cat("\n\n<b>===HOMOGENEITY OF VARIANCE ASSUMPTION===</b>\n\n")
      # 
      # df <- model_data %>%
      #     group_by(Measurement) %>%
      #     levene_test(formula = as.formula(paste0(metric, "~ Group"))) 
      # 
      # df %>% 
      #   kable(escape = F, digits = 3,
      #         caption = "Levene test (equality of variances)") %>%
      #   kable_classic_2(full_width = F) %>% 
      #   kable_styling() %>% 
      #   row_spec(
      #     which(df$p <= 0.05), bold = T, 
      #     background = red_color) %>% 
      #   print()
      # 
      # cat('\n\n')
      
      cat("##### LMM\n")
      
      model_data <- model_data %>% 
        mutate(AnimalTrial = paste(Animal, TrialNumber, sep = "_"))
      
      model_final <- lme(
        fixed = as.formula(paste0(metric, "~ Group*Measurement")),
        random = (~1|AnimalTrial),
        data = model_data)
      
      cat(paste0("`", ". ", capture.output(summary(model_final)), "`  \n"))
      
      
      # tab_model(
      #   model_final, show.stat = TRUE,
      #   show.aic = TRUE, title = "Summary of the LMM", 
      #   use.viewer = FALSE)
      
      # Sys.sleep(1)
      
      # htmltools::includeHTML("temp1.html") %>% 
      #   cat()
      
      # file.remove("temp.html")
      
      cat('\n\n')
      
      # cat("##### ANOVA\n")
      # 
      # model_aov <- anova.lme(model_final, type = "marginal")
      # 
      # df <- get_anova_table(model_aov) %>%
      #   data.frame()
      # 
      # df %>%
      #   kable(escape = F, digits = 4,
      #         caption = "Mixed ANOVA") %>%
      #   kable_classic_2(full_width = F) %>%
      #   kable_styling() %>%
      #   row_spec(
      #     which(df$p.value <= 0.05), bold = T,
      #     background = green_color) %>%
      #   print()
      # 
      # cat('\n\n')
      
      cat("##### Residuals check\n")
      
      res <- residuals(model_final)
      
      p1 <- ggplot(data = data.frame(residuals = res)) +
        geom_histogram(aes(x = residuals), bins = 25,
                       fill = "lightblue", color = "black") +
        labs(title = "Histogram of Residuals")
      
      p2 <- ggplot(
        data = data.frame(residuals = res),
        aes(sample = residuals)) +
        stat_qq() +
        stat_qq_line() +
        labs(title = "QQ Plot of Residuals")
      
      grid.arrange(p1, p2, nrow = 1)
      
      p1 <- plot(model_final, resid(.) ~ fitted(.), abline=0, main = "All Data")
      p2 <- plot(model_final, resid(.) ~ fitted(.)|Animal, abline=0, main = "By Animal")
      
      grid.arrange(p1, p2, nrow = 1, widths = c(1.5,2))
      
      cat('\n\n')
      
      cat("##### Effects\n")
      
      p1 <- emmip(model_final, formula = Group ~ Measurement) +
        theme(aspect.ratio = 1)
      
      p2 <- emmip(model_final, formula = Measurement ~ Group) +
        theme(aspect.ratio = 1)
      
      grid.arrange(p1, p2, nrow = 1)
      
      cat('\n\n')
      
      cat("##### Post-hoc tests\n")
      
      # cat("\n\n<b>===SIMPLE EFFECT FOR MEASUREMENT===</b>\n\n")
      
      # df <- pairs(emmeans(model_final, ~ Measurement | Group), p.adjust = "tukey") %>%
      #   data.frame()
      
      grp_eff <- pairs(emmeans(model_final, ~ Group | Measurement))
      msrmnt_eff <- pairs(emmeans(model_final, ~ Measurement | Group))
      df1 <- rbind(grp_eff, msrmnt_eff, adjust = "none") %>% 
        data.frame()
      
      df2 <- rbind(grp_eff, msrmnt_eff, adjust = "holm") %>% 
        data.frame() %>% 
        mutate(p.value.adj = p.value) %>% 
        select(-p.value)
      
      df <- df1 %>% 
        left_join(df2)
      
      df <- df %>% bind_cols(
        t_to_d(t = df$t.ratio, df_error = df$df) %>%
          data.frame() %>%
          round(2) %>%
          dplyr::select(d)) %>%
        mutate(eff_size = interpret_d(d)) %>%
        dplyr::select(-c(df))
      
      df %>%
        kable(escape = F, digits = 4, caption = "Multiple Comparisons") %>%
        kable_classic_2(full_width = F) %>%
        footnote(general = "P value adjustment: holm method for 9 tests") %>%
        kable_styling() %>%
        row_spec(
          which(df$p.value.adj < 0.05), bold = T,
          background = "#d6f5d6") %>% 
        print()
      
      # cat("\n\n<b>===SIMPLE EFFECT FOR GROUP===</b>\n\n")
      # 
      # df <- pairs(lsmeans(model_final, ~ Group | Measurement), adjust = "holm") %>%
      #   data.frame()
      # 
      # df <- df %>% bind_cols(
      #   t_to_d(t = df$t.ratio, df_error = df$df) %>%
      #     data.frame() %>%
      #     round(2) %>%
      #     # mutate(d_CI = paste0("[", CI_low, ", ", CI_high, "]")) %>%
      #     dplyr::select(d)) %>%
      #   mutate(eff_size = interpret_d(d)) %>%
      #   dplyr::select(-c(df))
      # 
      # df %>%
      #   kable(escape = F, digits = 4, caption = "Multiple Comparisons (between Groups)") %>%
      #   kable_classic_2(full_width = F) %>%
      #   footnote(general = "P value adjustment: tukey method for comparing a family of 3 estimates") %>%
      #   kable_styling() %>%
      #   row_spec(
      #     which(df$p.value < 0.05), bold = T,
      #     background = "#d6f5d6") %>% 
      #   print()
      
      cat('\n\n')
    }
    cat('\n\n')
  }
}

5 Hz Frequency

All Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIT KIT11 postLaser 44 0.001085 40 0.001027 -6.880854
KIC KIC15 postLaser 36 0.004629 22 0.001863 -6.285366
KIV KIV04 postLaser 21 0.001608 63 0.001021 -6.887303
KIC KIC14 preLaser 23 0.001612 131 0.001114 -6.799654
KIC KIC13 preLaser 4 0.001391 42 0.000807 -7.122803

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -23990.44 -23945.72 12003.22
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0003131318 0.0004704397
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0008261732 2.668446e-05 1276 30.960838 0e+00
. GroupKIC 0.0003943571 3.753280e-05 1276 10.507001 0e+00
. GroupKIV 0.0004200802 4.085064e-05 1276 10.283319 0e+00
. MeasurementpreLaser 0.0001016692 3.824049e-05 702 2.658680 8e-03
. GroupKIC:MeasurementpreLaser -0.0001943740 5.343178e-05 702 -3.637797 3e-04
. GroupKIV:MeasurementpreLaser -0.0002549151 5.798378e-05 702 -4.396318 0e+00
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.711
. GroupKIV -0.653 0.464
. MeasurementpreLaser -0.496 0.353 0.324
. GroupKIC:MeasurementpreLaser 0.355 -0.499 -0.232 -0.716
. GroupKIV:MeasurementpreLaser 0.327 -0.233 -0.499 -0.660 0.472
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.1149668 -0.5477251 -0.1718446 0.3533899 5.3131677
.
. Number of Observations: 1984
. Number of Groups: 1279

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -4e-04 0e+00 -10.5070 0.0000 0.0000 -0.59 medium
postLaser . KIT - KIV -4e-04 0e+00 -10.2833 0.0000 0.0000 -0.58 medium
postLaser . KIC - KIV 0e+00 0e+00 -0.6326 0.5271 0.9913 -0.04 very small
preLaser . KIT - KIC -2e-04 0e+00 -4.2037 0.0000 0.0002 -0.32 small
preLaser . KIT - KIV -2e-04 1e-04 -3.1971 0.0015 0.0073 -0.24 small
preLaser . KIC - KIV 0e+00 1e-04 0.6817 0.4956 0.9913 0.05 very small
. KIT postLaser - preLaser -1e-04 0e+00 -2.6587 0.0080 0.0321 -0.20 small
. KIC postLaser - preLaser 1e-04 0e+00 2.4842 0.0132 0.0396 0.19 very small
. KIV postLaser - preLaser 2e-04 0e+00 3.5159 0.0005 0.0028 0.27 small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 19 0.003038 30 0.001541 -6.475114 KIC04_19
KIT KIT03 postLaser 17 0.002507 30 0.001035 -6.873606 KIT03_17
KIV KIV16 preLaser 9 0.001259 96 0.000859 -7.060170 KIV16_9
KIT KIT07 preLaser 26 0.000573 54 0.000317 -8.055865 KIT07_26
KIT KIT11 preLaser 16 0.001137 43 0.000665 -7.315443 KIT11_16

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 2649.359 2694.078 -1316.679
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.3320418 0.3566372
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.209822 0.02295842 1276 -314.03819 0e+00
. GroupKIC 0.384048 0.03229457 1276 11.89202 0e+00
. GroupKIV 0.370291 0.03515879 1276 10.53196 0e+00
. MeasurementpreLaser 0.119430 0.02967139 702 4.02510 1e-04
. GroupKIC:MeasurementpreLaser -0.218027 0.04142756 702 -5.26285 0e+00
. GroupKIV:MeasurementpreLaser -0.189782 0.04492335 702 -4.22458 0e+00
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.711
. GroupKIV -0.653 0.464
. MeasurementpreLaser -0.433 0.308 0.283
. GroupKIC:MeasurementpreLaser 0.310 -0.435 -0.202 -0.716
. GroupKIV:MeasurementpreLaser 0.286 -0.203 -0.434 -0.660 0.473
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.30637056 -0.55408521 -0.02050709 0.50472441 2.94778547
.
. Number of Observations: 1984
. Number of Groups: 1279

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.3840 0.0323 -11.8920 0.0000 0.0000 -0.67 medium
postLaser . KIT - KIV -0.3703 0.0352 -10.5320 0.0000 0.0000 -0.59 medium
postLaser . KIC - KIV 0.0138 0.0350 0.3931 0.6943 1.0000 0.02 very small
preLaser . KIT - KIC -0.1660 0.0399 -4.1571 0.0000 0.0002 -0.31 small
preLaser . KIT - KIV -0.1805 0.0434 -4.1611 0.0000 0.0002 -0.31 small
preLaser . KIC - KIV -0.0145 0.0429 -0.3376 0.7357 1.0000 -0.03 very small
. KIT postLaser - preLaser -0.1194 0.0297 -4.0251 0.0001 0.0003 -0.30 small
. KIC postLaser - preLaser 0.0986 0.0289 3.4103 0.0007 0.0027 0.26 small
. KIV postLaser - preLaser 0.0704 0.0337 2.0857 0.0374 0.1121 0.16 very small
Note:
P value adjustment: holm method for 9 tests

I_II Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 10 0.002150 163 0.001082 -6.829147
KIT KIT03 preLaser 14 0.001816 53 0.000818 -7.108336
KIV KIV12 postLaser 46 0.002304 31 0.000517 -7.567494
KIT KIT07 postLaser 37 0.000820 123 0.000271 -8.213857
KIT KIT11 preLaser 17 0.000838 82 0.000722 -7.233258

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -21819.34 -21774.56 10917.67
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0005017833 0.0008836926
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0007260017 4.866143e-05 1265 14.919448 0.0000
. GroupKIC 0.0003862483 6.715415e-05 1265 5.751667 0.0000
. GroupKIV 0.0007866637 7.338918e-05 1265 10.719070 0.0000
. MeasurementpreLaser -0.0000351233 7.180804e-05 729 -0.489128 0.6249
. GroupKIC:MeasurementpreLaser 0.0000986259 9.893027e-05 729 0.996923 0.3191
. GroupKIV:MeasurementpreLaser -0.0000192205 1.086651e-04 729 -0.176879 0.8597
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.725
. GroupKIV -0.663 0.480
. MeasurementpreLaser -0.514 0.372 0.341
. GroupKIC:MeasurementpreLaser 0.373 -0.515 -0.247 -0.726
. GroupKIV:MeasurementpreLaser 0.339 -0.246 -0.513 -0.661 0.480
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.2237387 -0.5075486 -0.1929080 0.2294810 8.3867142
.
. Number of Observations: 2000
. Number of Groups: 1268

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -4e-04 1e-04 -5.7517 0.0000 0.0000 -0.32 small
postLaser . KIT - KIV -8e-04 1e-04 -10.7191 0.0000 0.0000 -0.60 medium
postLaser . KIC - KIV -4e-04 1e-04 -5.5744 0.0000 0.0000 -0.31 small
preLaser . KIT - KIC -5e-04 1e-04 -5.6147 0.0000 0.0000 -0.42 small
preLaser . KIT - KIV -8e-04 1e-04 -8.0810 0.0000 0.0000 -0.60 medium
preLaser . KIC - KIV -3e-04 1e-04 -3.0457 0.0024 0.0096 -0.23 small
. KIT postLaser - preLaser 0e+00 1e-04 0.4891 0.6249 1.0000 0.04 very small
. KIC postLaser - preLaser -1e-04 1e-04 -0.9332 0.3510 1.0000 -0.07 very small
. KIV postLaser - preLaser 1e-04 1e-04 0.6663 0.5054 1.0000 0.05 very small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 10 0.002150 163 0.001082 -6.829147 KIC04_10
KIT KIT03 preLaser 14 0.001816 53 0.000818 -7.108336 KIT03_14
KIV KIV12 postLaser 46 0.002304 31 0.000517 -7.567494 KIV12_46
KIT KIT07 postLaser 37 0.000820 123 0.000271 -8.213857 KIT07_37
KIT KIT11 preLaser 17 0.000838 82 0.000722 -7.233258 KIT11_17

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 4390.243 4435.026 -2187.121
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.4296398 0.5962036
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.391098 0.03518502 1265 -210.06375 0.0000
. GroupKIC 0.328863 0.04855526 1265 6.77297 0.0000
. GroupKIV 0.478623 0.05306111 1265 9.02022 0.0000
. MeasurementpreLaser -0.051243 0.04904068 729 -1.04491 0.2964
. GroupKIC:MeasurementpreLaser 0.095759 0.06756067 729 1.41738 0.1568
. GroupKIV:MeasurementpreLaser -0.008918 0.07423666 729 -0.12013 0.9044
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.725
. GroupKIV -0.663 0.481
. MeasurementpreLaser -0.474 0.343 0.314
. GroupKIC:MeasurementpreLaser 0.344 -0.475 -0.228 -0.726
. GroupKIV:MeasurementpreLaser 0.313 -0.227 -0.473 -0.661 0.480
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.33588823 -0.61583578 -0.02496457 0.55469020 2.85699199
.
. Number of Observations: 2000
. Number of Groups: 1268

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.3289 0.0486 -6.7730 0.0000 0.00 -0.38 small
postLaser . KIT - KIV -0.4786 0.0531 -9.0202 0.0000 0.00 -0.51 medium
postLaser . KIC - KIV -0.1498 0.0519 -2.8837 0.0040 0.02 -0.16 very small
preLaser . KIT - KIC -0.4246 0.0617 -6.8832 0.0000 0.00 -0.51 medium
preLaser . KIT - KIV -0.4697 0.0678 -6.9254 0.0000 0.00 -0.51 medium
preLaser . KIC - KIV -0.0451 0.0663 -0.6804 0.4965 1.00 -0.05 very small
. KIT postLaser - preLaser 0.0512 0.0490 1.0449 0.2964 1.00 0.08 very small
. KIC postLaser - preLaser -0.0445 0.0465 -0.9580 0.3384 1.00 -0.07 very small
. KIV postLaser - preLaser 0.0602 0.0557 1.0795 0.2807 1.00 0.08 very small
Note:
P value adjustment: holm method for 9 tests

IV Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 19 0.005478 30 0.002165 -6.135261
KIV KIV12 preLaser 3 0.002766 28 0.000871 -7.046414
KIT KIT05 postLaser 47 0.007739 49 0.003304 -5.712621
KIT KIT08 postLaser 4 0.002820 48 0.001233 -6.698080
KIT KIT08 postLaser 19 0.001781 54 0.000925 -6.985926

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -21752.74 -21707.66 10884.37
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0006469602 0.001083729
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0009639688 5.787873e-05 1311 16.654976 0.0000
. GroupKIC 0.0006076031 8.168478e-05 1311 7.438388 0.0000
. GroupKIV 0.0007695869 8.933035e-05 1311 8.615066 0.0000
. MeasurementpreLaser 0.0002488964 8.429681e-05 758 2.952619 0.0032
. GroupKIC:MeasurementpreLaser -0.0002864282 1.183665e-04 758 -2.419842 0.0158
. GroupKIV:MeasurementpreLaser -0.0004275633 1.304292e-04 758 -3.278125 0.0011
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.709
. GroupKIV -0.648 0.459
. MeasurementpreLaser -0.511 0.362 0.331
. GroupKIC:MeasurementpreLaser 0.364 -0.513 -0.236 -0.712
. GroupKIV:MeasurementpreLaser 0.330 -0.234 -0.507 -0.646 0.460
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.0026699 -0.5091244 -0.2501816 0.2181196 5.5888554
.
. Number of Observations: 2075
. Number of Groups: 1314

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -6e-04 1e-04 -7.4384 0.0000 0.0000 -0.41 small
postLaser . KIT - KIV -8e-04 1e-04 -8.6151 0.0000 0.0000 -0.48 small
postLaser . KIC - KIV -2e-04 1e-04 -1.8164 0.0695 0.2781 -0.10 very small
preLaser . KIT - KIC -3e-04 1e-04 -3.0964 0.0020 0.0142 -0.22 small
preLaser . KIT - KIV -3e-04 1e-04 -2.9806 0.0030 0.0178 -0.22 small
preLaser . KIC - KIV 0e+00 1e-04 -0.1829 0.8549 1.0000 -0.01 very small
. KIT postLaser - preLaser -2e-04 1e-04 -2.9526 0.0032 0.0178 -0.21 small
. KIC postLaser - preLaser 0e+00 1e-04 0.4517 0.6516 1.0000 0.03 very small
. KIV postLaser - preLaser 2e-04 1e-04 1.7951 0.0730 0.2781 0.13 very small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 19 0.005478 30 0.002165 -6.135261 KIC04_19
KIV KIV12 preLaser 3 0.002766 28 0.000871 -7.046414 KIV12_3
KIT KIT05 postLaser 47 0.007739 49 0.003304 -5.712621 KIT05_47
KIT KIT08 postLaser 4 0.002820 48 0.001233 -6.698080 KIT08_4
KIT KIT08 postLaser 19 0.001781 54 0.000925 -6.985926 KIT08_19

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 4859.403 4904.482 -2421.702
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.5146166 0.6131172
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.263620 0.03667633 1311 -198.04652 0
. GroupKIC 0.513803 0.05176443 1311 9.92580 0
. GroupKIV 0.561260 0.05662912 1311 9.91115 0
. MeasurementpreLaser 0.268867 0.04863053 758 5.52878 0
. GroupKIC:MeasurementpreLaser -0.380390 0.06824862 758 -5.57359 0
. GroupKIV:MeasurementpreLaser -0.343579 0.07519910 758 -4.56892 0
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.709
. GroupKIV -0.648 0.459
. MeasurementpreLaser -0.450 0.319 0.291
. GroupKIC:MeasurementpreLaser 0.321 -0.452 -0.208 -0.713
. GroupKIV:MeasurementpreLaser 0.291 -0.206 -0.446 -0.647 0.461
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.42036089 -0.56040315 -0.00855083 0.53341613 2.55454098
.
. Number of Observations: 2075
. Number of Groups: 1314

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.5138 0.0518 -9.9258 0.0000 0.0000 -0.55 medium
postLaser . KIT - KIV -0.5613 0.0566 -9.9111 0.0000 0.0000 -0.55 medium
postLaser . KIC - KIV -0.0475 0.0565 -0.8394 0.4014 0.5794 -0.05 very small
preLaser . KIT - KIC -0.1334 0.0644 -2.0722 0.0386 0.1543 -0.15 very small
preLaser . KIT - KIV -0.2177 0.0712 -3.0582 0.0023 0.0138 -0.22 small
preLaser . KIC - KIV -0.0843 0.0707 -1.1917 0.2338 0.5794 -0.09 very small
. KIT postLaser - preLaser -0.2689 0.0486 -5.5288 0.0000 0.0000 -0.40 small
. KIC postLaser - preLaser 0.1115 0.0479 2.3290 0.0201 0.1006 0.17 very small
. KIV postLaser - preLaser 0.0747 0.0574 1.3025 0.1931 0.5794 0.09 very small
Note:
P value adjustment: holm method for 9 tests

V Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 18 0.001327 177 0.000672 -7.304889
KIV KIV12 preLaser 9 0.002468 31 0.000955 -6.953277
KIT KIT05 postLaser 37 0.002737 35 0.001137 -6.779706
KIT KIT08 preLaser 28 0.003772 59 0.001679 -6.389323
KIT KIT08 postLaser 15 0.000688 6 0.000275 -8.197161

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -25390.56 -25345.51 12703.28
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0002713318 0.0004348682
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0006385442 2.342775e-05 1307 27.255888 0.0000
. GroupKIC 0.0002655750 3.311974e-05 1307 8.018633 0.0000
. GroupKIV 0.0003793052 3.650220e-05 1307 10.391297 0.0000
. MeasurementpreLaser 0.0000705934 3.398077e-05 754 2.077453 0.0381
. GroupKIC:MeasurementpreLaser -0.0002315314 4.776022e-05 754 -4.847788 0.0000
. GroupKIV:MeasurementpreLaser -0.0002696826 5.243235e-05 754 -5.143439 0.0000
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.707
. GroupKIV -0.642 0.454
. MeasurementpreLaser -0.502 0.355 0.322
. GroupKIC:MeasurementpreLaser 0.357 -0.504 -0.229 -0.711
. GroupKIV:MeasurementpreLaser 0.325 -0.230 -0.506 -0.648 0.461
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.0343731 -0.6089049 -0.1215587 0.3947961 7.4674104
.
. Number of Observations: 2067
. Number of Groups: 1310

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -3e-04 0 -8.0186 0.0000 0.0000 -0.44 small
postLaser . KIT - KIV -4e-04 0 -10.3913 0.0000 0.0000 -0.57 medium
postLaser . KIC - KIV -1e-04 0 -3.1166 0.0019 0.0093 -0.17 very small
preLaser . KIT - KIC 0e+00 0 -0.8058 0.4206 0.4206 -0.06 very small
preLaser . KIT - KIV -1e-04 0 -2.3661 0.0182 0.0729 -0.17 very small
preLaser . KIC - KIV -1e-04 0 -1.6404 0.1013 0.2027 -0.12 very small
. KIT postLaser - preLaser -1e-04 0 -2.0775 0.0381 0.1143 -0.15 very small
. KIC postLaser - preLaser 2e-04 0 4.7954 0.0000 0.0000 0.35 small
. KIV postLaser - preLaser 2e-04 0 4.9859 0.0000 0.0000 0.36 small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 18 0.001327 177 0.000672 -7.304889 KIC04_18
KIV KIV12 preLaser 9 0.002468 31 0.000955 -6.953277 KIV12_9
KIT KIT05 postLaser 37 0.002737 35 0.001137 -6.779706 KIT05_37
KIT KIT08 preLaser 28 0.003772 59 0.001679 -6.389323 KIT08_28
KIT KIT08 postLaser 15 0.000688 6 0.000275 -8.197161 KIT08_15

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 3852.364 3897.411 -1918.182
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.3461334 0.514424
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.533532 0.02833449 1307 -265.87854 0.0000
. GroupKIC 0.326223 0.04005786 1307 8.14381 0.0000
. GroupKIV 0.417356 0.04414884 1307 9.45339 0.0000
. MeasurementpreLaser 0.115640 0.04036792 754 2.86466 0.0043
. GroupKIC:MeasurementpreLaser -0.256347 0.05672703 754 -4.51895 0.0000
. GroupKIV:MeasurementpreLaser -0.251855 0.06227222 754 -4.04441 0.0001
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.707
. GroupKIV -0.642 0.454
. MeasurementpreLaser -0.490 0.346 0.314
. GroupKIC:MeasurementpreLaser 0.348 -0.491 -0.224 -0.712
. GroupKIV:MeasurementpreLaser 0.317 -0.224 -0.493 -0.648 0.461
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.71469205 -0.61019927 0.08666851 0.59529352 2.64954072
.
. Number of Observations: 2067
. Number of Groups: 1310

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.3262 0.0401 -8.1438 0.0000 0.0000 -0.45 small
postLaser . KIT - KIV -0.4174 0.0441 -9.4534 0.0000 0.0000 -0.52 medium
postLaser . KIC - KIV -0.0911 0.0441 -2.0648 0.0391 0.1174 -0.11 very small
preLaser . KIT - KIC -0.0699 0.0509 -1.3727 0.1702 0.1708 -0.10 very small
preLaser . KIT - KIV -0.1655 0.0558 -2.9646 0.0031 0.0188 -0.22 small
preLaser . KIC - KIV -0.0956 0.0555 -1.7224 0.0854 0.1708 -0.13 very small
. KIT postLaser - preLaser -0.1156 0.0404 -2.8647 0.0043 0.0209 -0.21 small
. KIC postLaser - preLaser 0.1407 0.0399 3.5305 0.0004 0.0031 0.26 small
. KIV postLaser - preLaser 0.1362 0.0474 2.8728 0.0042 0.0209 0.21 small
Note:
P value adjustment: holm method for 9 tests

VI Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 14 0.001158 107 0.000491 -7.619589
KIV KIV09 postLaser 25 0.002383 47 0.001039 -6.869694
KIT KIT05 postLaser 28 0.000699 96 0.000361 -7.927456
KIT KIT08 preLaser 12 0.001564 47 0.000555 -7.497265
KIT KIT08 preLaser 28 0.003388 42 0.001942 -6.244184

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -26822.12 -26776.95 13419.06
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0002083732 0.0003398995
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0006161053 1.806346e-05 1315 34.10781 0.0000
. GroupKIC 0.0001200669 2.559744e-05 1315 4.69058 0.0000
. GroupKIV 0.0001279863 2.812396e-05 1315 4.55079 0.0000
. MeasurementpreLaser 0.0000768753 2.608973e-05 777 2.94657 0.0033
. GroupKIC:MeasurementpreLaser -0.0001508542 3.687570e-05 777 -4.09088 0.0000
. GroupKIV:MeasurementpreLaser -0.0000835693 4.059913e-05 777 -2.05840 0.0399
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.706
. GroupKIV -0.642 0.453
. MeasurementpreLaser -0.504 0.356 0.324
. GroupKIC:MeasurementpreLaser 0.357 -0.506 -0.229 -0.708
. GroupKIV:MeasurementpreLaser 0.324 -0.229 -0.505 -0.643 0.455
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.2856561 -0.5886031 -0.1898624 0.3731704 6.5180427
.
. Number of Observations: 2098
. Number of Groups: 1318

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -1e-04 0 -4.6906 0.0000 0.0000 -0.26 small
postLaser . KIT - KIV -1e-04 0 -4.5508 0.0000 0.0000 -0.25 small
postLaser . KIC - KIV 0e+00 0 -0.2811 0.7787 1.0000 -0.02 very small
preLaser . KIT - KIC 0e+00 0 0.9458 0.3446 1.0000 0.07 very small
preLaser . KIT - KIV 0e+00 0 -1.2380 0.2161 0.8643 -0.09 very small
preLaser . KIC - KIV -1e-04 0 -2.0989 0.0362 0.1808 -0.15 very small
. KIT postLaser - preLaser -1e-04 0 -2.9466 0.0033 0.0232 -0.21 small
. KIC postLaser - preLaser 1e-04 0 2.8388 0.0046 0.0279 0.20 small
. KIV postLaser - preLaser 0e+00 0 0.2152 0.8297 1.0000 0.02 very small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 14 0.001158 107 0.000491 -7.619589 KIC04_14
KIV KIV09 postLaser 25 0.002383 47 0.001039 -6.869694 KIV09_25
KIT KIT05 postLaser 28 0.000699 96 0.000361 -7.927456 KIT05_28
KIT KIT08 preLaser 12 0.001564 47 0.000555 -7.497265 KIT08_12
KIT KIT08 preLaser 28 0.003388 42 0.001942 -6.244184 KIT08_28

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 3287.523 3332.69 -1635.761
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.283776 0.4508396
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.546088 0.02413565 1315 -312.65320 0.0000
. GroupKIC 0.183366 0.03420213 1315 5.36126 0.0000
. GroupKIV 0.232284 0.03757814 1315 6.18136 0.0000
. MeasurementpreLaser 0.084472 0.03464979 777 2.43787 0.0150
. GroupKIC:MeasurementpreLaser -0.164101 0.04897422 777 -3.35076 0.0008
. GroupKIV:MeasurementpreLaser -0.103587 0.05391930 777 -1.92115 0.0551
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.706
. GroupKIV -0.642 0.453
. MeasurementpreLaser -0.500 0.353 0.321
. GroupKIC:MeasurementpreLaser 0.354 -0.502 -0.227 -0.708
. GroupKIV:MeasurementpreLaser 0.321 -0.227 -0.500 -0.643 0.455
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.82557346 -0.59703983 0.01127123 0.59181776 3.25777142
.
. Number of Observations: 2098
. Number of Groups: 1318

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.1834 0.0342 -5.3613 0.0000 0.0000 -0.30 small
postLaser . KIT - KIV -0.2323 0.0376 -6.1814 0.0000 0.0000 -0.34 small
postLaser . KIC - KIV -0.0489 0.0376 -1.2996 0.1940 0.5819 -0.07 very small
preLaser . KIT - KIC -0.0193 0.0434 -0.4435 0.6576 1.0000 -0.03 very small
preLaser . KIT - KIV -0.1287 0.0479 -2.6880 0.0073 0.0514 -0.19 very small
preLaser . KIC - KIV -0.1094 0.0478 -2.2885 0.0224 0.1084 -0.16 very small
. KIT postLaser - preLaser -0.0845 0.0346 -2.4379 0.0150 0.0900 -0.17 very small
. KIC postLaser - preLaser 0.0796 0.0346 2.3007 0.0217 0.1084 0.17 very small
. KIV postLaser - preLaser 0.0191 0.0413 0.4627 0.6437 1.0000 0.03 very small
Note:
P value adjustment: holm method for 9 tests

10 Hz Frequency

All Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 29 0.003749 67 0.002187 -6.125174
KIT KIT04 postLaser 3 0.001043 33 0.000487 -7.626256
KIT KIT09 postLaser 3 0.000619 40 0.000421 -7.772903
KIV KIV02 postLaser 21 0.004219 53 0.002644 -5.935353
KIT KIT12 postLaser 12 0.000641 27 0.000474 -7.653563

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -20807.02 -20763.14 10411.51
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0003522518 0.0006056711
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0009795107 3.587834e-05 1196 27.300895 0.0000
. GroupKIC 0.0005205665 4.911419e-05 1196 10.599106 0.0000
. GroupKIV 0.0004508468 5.311675e-05 1196 8.487846 0.0000
. MeasurementpreLaser 0.0001612590 5.445926e-05 585 2.961095 0.0032
. GroupKIC:MeasurementpreLaser -0.0003192589 7.425261e-05 585 -4.299632 0.0000
. GroupKIV:MeasurementpreLaser -0.0003172205 7.891861e-05 585 -4.019590 0.0001
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.731
. GroupKIV -0.675 0.493
. MeasurementpreLaser -0.510 0.373 0.345
. GroupKIC:MeasurementpreLaser 0.374 -0.511 -0.253 -0.733
. GroupKIV:MeasurementpreLaser 0.352 -0.257 -0.519 -0.690 0.506
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.0773631 -0.5762149 -0.1981115 0.3402905 5.1344536
.
. Number of Observations: 1787
. Number of Groups: 1199

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -5e-04 0e+00 -10.5991 0.0000 0.0000 -0.61 medium
postLaser . KIT - KIV -5e-04 1e-04 -8.4878 0.0000 0.0000 -0.49 small
postLaser . KIC - KIV 1e-04 1e-04 1.3520 0.1766 0.3532 0.08 very small
preLaser . KIT - KIC -2e-04 1e-04 -3.1068 0.0020 0.0128 -0.26 small
preLaser . KIT - KIV -1e-04 1e-04 -1.9492 0.0518 0.1553 -0.16 very small
preLaser . KIC - KIV 1e-04 1e-04 1.0227 0.3069 0.3532 0.08 very small
. KIT postLaser - preLaser -2e-04 1e-04 -2.9611 0.0032 0.0159 -0.24 small
. KIC postLaser - preLaser 2e-04 1e-04 3.1303 0.0018 0.0128 0.26 small
. KIV postLaser - preLaser 2e-04 1e-04 2.7306 0.0065 0.0261 0.23 small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 29 0.003749 67 0.002187 -6.125174 KIC04_29
KIT KIT04 postLaser 3 0.001043 33 0.000487 -7.626256 KIT04_3
KIT KIT09 postLaser 3 0.000619 40 0.000421 -7.772903 KIT09_3
KIV KIV02 postLaser 21 0.004219 53 0.002644 -5.935353 KIV02_21
KIT KIT12 postLaser 12 0.000641 27 0.000474 -7.653563 KIT12_12

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 2568.136 2612.016 -1276.068
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.2839713 0.4110964
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.047648 0.02555557 1196 -275.77739 0
. GroupKIC 0.439626 0.03498536 1196 12.56601 0
. GroupKIV 0.330021 0.03783738 1196 8.72209 0
. MeasurementpreLaser 0.166244 0.03744173 585 4.44006 0
. GroupKIC:MeasurementpreLaser -0.325750 0.05103216 585 -6.38323 0
. GroupKIV:MeasurementpreLaser -0.241066 0.05419492 585 -4.44812 0
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.730
. GroupKIV -0.675 0.493
. MeasurementpreLaser -0.485 0.354 0.327
. GroupKIC:MeasurementpreLaser 0.356 -0.485 -0.240 -0.734
. GroupKIV:MeasurementpreLaser 0.335 -0.245 -0.493 -0.691 0.507
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.41793264 -0.57480444 -0.04191804 0.53769152 2.95418415
.
. Number of Observations: 1787
. Number of Groups: 1199

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.4396 0.0350 -12.5660 0.0000 0.0000 -0.73 medium
postLaser . KIT - KIV -0.3300 0.0378 -8.7221 0.0000 0.0000 -0.50 medium
postLaser . KIC - KIV 0.1096 0.0367 2.9837 0.0029 0.0145 0.17 very small
preLaser . KIT - KIC -0.1139 0.0458 -2.4879 0.0131 0.0525 -0.21 small
preLaser . KIT - KIV -0.0890 0.0485 -1.8360 0.0669 0.1700 -0.15 very small
preLaser . KIC - KIV 0.0249 0.0468 0.5328 0.5944 0.5944 0.04 very small
. KIT postLaser - preLaser -0.1662 0.0374 -4.4401 0.0000 0.0001 -0.37 small
. KIC postLaser - preLaser 0.1595 0.0347 4.6000 0.0000 0.0000 0.38 small
. KIV postLaser - preLaser 0.0748 0.0392 1.9096 0.0567 0.1700 0.16 very small
Note:
P value adjustment: holm method for 9 tests

I_II Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 31 0.004156 20 0.002444 -6.014108
KIT KIT05 preLaser 27 0.002800 32 0.001150 -6.767687
KIV KIV17 postLaser 43 0.001107 93 0.000516 -7.568471
KIT KIT09 preLaser 29 0.001393 46 0.000775 -7.162432
KIT KIT12 postLaser 40 0.000559 39 0.000240 -8.335982

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -19538.11 -19493.97 9777.054
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0006521277 0.001006262
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0007071523 5.968008e-05 1211 11.849051 0.0000
. GroupKIC 0.0004798503 8.380398e-05 1211 5.725866 0.0000
. GroupKIV 0.0009261064 8.931221e-05 1211 10.369315 0.0000
. MeasurementpreLaser 0.0000412080 8.546227e-05 629 0.482178 0.6298
. GroupKIC:MeasurementpreLaser -0.0000237852 1.190341e-04 629 -0.199819 0.8417
. GroupKIV:MeasurementpreLaser 0.0001122388 1.281510e-04 629 0.875832 0.3815
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.712
. GroupKIV -0.668 0.476
. MeasurementpreLaser -0.508 0.362 0.340
. GroupKIC:MeasurementpreLaser 0.365 -0.520 -0.244 -0.718
. GroupKIV:MeasurementpreLaser 0.339 -0.241 -0.502 -0.667 0.479
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.3214585 -0.4908675 -0.2014684 0.1817366 5.3029704
.
. Number of Observations: 1846
. Number of Groups: 1214

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -5e-04 1e-04 -5.7259 0.0000 0.0000 -0.33 small
postLaser . KIT - KIV -9e-04 1e-04 -10.3693 0.0000 0.0000 -0.60 medium
postLaser . KIC - KIV -4e-04 1e-04 -5.0283 0.0000 0.0000 -0.29 small
preLaser . KIT - KIC -5e-04 1e-04 -4.3861 0.0000 0.0001 -0.35 small
preLaser . KIT - KIV -1e-03 1e-04 -9.1428 0.0000 0.0000 -0.73 medium
preLaser . KIC - KIV -6e-04 1e-04 -5.2406 0.0000 0.0000 -0.42 small
. KIT postLaser - preLaser 0e+00 1e-04 -0.4822 0.6298 1.0000 -0.04 very small
. KIC postLaser - preLaser 0e+00 1e-04 -0.2103 0.8335 1.0000 -0.02 very small
. KIV postLaser - preLaser -2e-04 1e-04 -1.6069 0.1086 0.3257 -0.13 very small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 31 0.004156 20 0.002444 -6.014108 KIC04_31
KIT KIT05 preLaser 27 0.002800 32 0.001150 -6.767687 KIT05_27
KIV KIV17 postLaser 43 0.001107 93 0.000516 -7.568471 KIV17_43
KIT KIT09 preLaser 29 0.001393 46 0.000775 -7.162432 KIT09_29
KIT KIT12 postLaser 40 0.000559 39 0.000240 -8.335982 KIT12_40

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 4451.662 4495.802 -2217.831
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.4455501 0.68032
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.456540 0.04047281 1211 -184.23578 0.0000
. GroupKIC 0.387985 0.05683104 1211 6.82699 0.0000
. GroupKIV 0.648120 0.06056930 1211 10.70047 0.0000
. MeasurementpreLaser 0.016525 0.05781879 629 0.28581 0.7751
. GroupKIC:MeasurementpreLaser -0.097108 0.08053580 629 -1.20577 0.2284
. GroupKIV:MeasurementpreLaser -0.073241 0.08669632 629 -0.84480 0.3985
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.712
. GroupKIV -0.668 0.476
. MeasurementpreLaser -0.506 0.361 0.338
. GroupKIC:MeasurementpreLaser 0.364 -0.519 -0.243 -0.718
. GroupKIV:MeasurementpreLaser 0.338 -0.241 -0.501 -0.667 0.479
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.28739661 -0.58839451 -0.06166797 0.57239582 2.86478984
.
. Number of Observations: 1846
. Number of Groups: 1214

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.3880 0.0568 -6.8270 0.0000 0.0000 -0.39 small
postLaser . KIT - KIV -0.6481 0.0606 -10.7005 0.0000 0.0000 -0.61 medium
postLaser . KIC - KIV -0.2601 0.0602 -4.3222 0.0000 0.0001 -0.25 small
preLaser . KIT - KIC -0.2909 0.0705 -4.1270 0.0000 0.0002 -0.33 small
preLaser . KIT - KIV -0.5749 0.0770 -7.4678 0.0000 0.0000 -0.60 medium
preLaser . KIC - KIV -0.2840 0.0753 -3.7709 0.0002 0.0007 -0.30 small
. KIT postLaser - preLaser -0.0165 0.0578 -0.2858 0.7751 0.7751 -0.02 very small
. KIC postLaser - preLaser 0.0806 0.0561 1.4374 0.1511 0.4533 0.11 very small
. KIV postLaser - preLaser 0.0567 0.0646 0.8780 0.3803 0.7606 0.07 very small
Note:
P value adjustment: holm method for 9 tests

IV Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 13 0.004901 58 0.003140 -5.763490
KIV KIV12 preLaser 16 0.004216 31 0.001473 -6.520582
KIT KIT05 postLaser 42 0.000575 44 0.000295 -8.127092
KIT KIT08 postLaser 11 0.000850 66 0.000301 -8.110039
KIT KIT08 postLaser 26 0.000389 53 0.000188 -8.578559

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -20836.86 -20791.83 10426.43
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0009204071 0.001234504
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0011623743 7.100125e-05 1302 16.371180 0.0000
. GroupKIC 0.0008223065 1.000546e-04 1302 8.218581 0.0000
. GroupKIV 0.0007040249 1.098606e-04 1302 6.408348 0.0000
. MeasurementpreLaser 0.0002676947 9.737271e-05 753 2.749176 0.0061
. GroupKIC:MeasurementpreLaser -0.0004732709 1.367784e-04 753 -3.460128 0.0006
. GroupKIV:MeasurementpreLaser -0.0001636684 1.504508e-04 753 -1.087853 0.2770
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.710
. GroupKIV -0.646 0.459
. MeasurementpreLaser -0.478 0.339 0.309
. GroupKIC:MeasurementpreLaser 0.340 -0.478 -0.220 -0.712
. GroupKIV:MeasurementpreLaser 0.309 -0.219 -0.475 -0.647 0.461
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -1.9158406 -0.4917052 -0.2374318 0.2272450 4.1728245
.
. Number of Observations: 2061
. Number of Groups: 1305

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -8e-04 1e-04 -8.2186 0.0000 0.0000 -0.46 small
postLaser . KIT - KIV -7e-04 1e-04 -6.4083 0.0000 0.0000 -0.36 small
postLaser . KIC - KIV 1e-04 1e-04 1.0799 0.2804 0.5608 0.06 very small
preLaser . KIT - KIC -3e-04 1e-04 -2.7916 0.0054 0.0323 -0.20 small
preLaser . KIT - KIV -5e-04 1e-04 -3.9198 0.0001 0.0007 -0.29 small
preLaser . KIC - KIV -2e-04 1e-04 -1.3955 0.1633 0.4898 -0.10 very small
. KIT postLaser - preLaser -3e-04 1e-04 -2.7492 0.0061 0.0323 -0.20 small
. KIC postLaser - preLaser 2e-04 1e-04 2.1402 0.0327 0.1307 0.16 very small
. KIV postLaser - preLaser -1e-04 1e-04 -0.9070 0.3647 0.5608 -0.07 very small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 13 0.004901 58 0.003140 -5.763490 KIC04_13
KIV KIV12 preLaser 16 0.004216 31 0.001473 -6.520582 KIV12_16
KIT KIT05 postLaser 42 0.000575 44 0.000295 -8.127092 KIT05_42
KIT KIT08 postLaser 11 0.000850 66 0.000301 -8.110039 KIT08_11
KIT KIT08 postLaser 26 0.000389 53 0.000188 -8.578559 KIT08_26

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 5064.415 5109.439 -2524.207
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.5439578 0.6503434
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.107760 0.03907467 1302 -181.90201 0.0000
. GroupKIC 0.578474 0.05506625 1302 10.50505 0.0000
. GroupKIV 0.461336 0.06047068 1302 7.62909 0.0000
. MeasurementpreLaser 0.188077 0.05166173 753 3.64055 0.0003
. GroupKIC:MeasurementpreLaser -0.406389 0.07255643 753 -5.60100 0.0000
. GroupKIV:MeasurementpreLaser -0.137265 0.07979656 753 -1.72018 0.0858
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.710
. GroupKIV -0.646 0.459
. MeasurementpreLaser -0.455 0.323 0.294
. GroupKIC:MeasurementpreLaser 0.324 -0.456 -0.209 -0.712
. GroupKIV:MeasurementpreLaser 0.295 -0.209 -0.452 -0.647 0.461
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.68567501 -0.55922980 -0.02733962 0.54327811 2.35551088
.
. Number of Observations: 2061
. Number of Groups: 1305

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.5785 0.0551 -10.5050 0.0000 0.0000 -0.58 medium
postLaser . KIT - KIV -0.4613 0.0605 -7.6291 0.0000 0.0000 -0.42 small
postLaser . KIC - KIV 0.1171 0.0603 1.9428 0.0523 0.1277 0.11 very small
preLaser . KIT - KIC -0.1721 0.0682 -2.5220 0.0119 0.0475 -0.18 very small
preLaser . KIT - KIV -0.3241 0.0752 -4.3080 0.0000 0.0001 -0.31 small
preLaser . KIC - KIV -0.1520 0.0748 -2.0314 0.0426 0.1277 -0.15 very small
. KIT postLaser - preLaser -0.1881 0.0517 -3.6406 0.0003 0.0015 -0.27 small
. KIC postLaser - preLaser 0.2183 0.0509 4.2851 0.0000 0.0001 0.31 small
. KIV postLaser - preLaser -0.0508 0.0608 -0.8355 0.4037 0.4037 -0.06 very small
Note:
P value adjustment: holm method for 9 tests

V Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 12 0.002495 43 0.001855 -6.289737
KIT KIT03 preLaser 21 0.002094 34 0.000708 -7.253470
KIV KIV12 postLaser 4 0.001797 31 0.000885 -7.029949
KIT KIT05 postLaser 40 0.002731 52 0.001340 -6.614892
KIT KIT09 postLaser 12 0.000842 49 0.000564 -7.480192

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -23897.94 -23853.02 11956.97
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0003403101 0.0005751929
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0007881540 3.087190e-05 1288 25.529819 0.0000
. GroupKIC 0.0002719351 4.363765e-05 1288 6.231662 0.0000
. GroupKIV 0.0004990980 4.817425e-05 1288 10.360266 0.0000
. MeasurementpreLaser 0.0000329399 4.520048e-05 740 0.728751 0.4664
. GroupKIC:MeasurementpreLaser -0.0002013532 6.324859e-05 740 -3.183521 0.0015
. GroupKIV:MeasurementpreLaser -0.0003035781 6.996207e-05 740 -4.339182 0.0000
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.707
. GroupKIV -0.641 0.453
. MeasurementpreLaser -0.512 0.362 0.328
. GroupKIC:MeasurementpreLaser 0.366 -0.517 -0.234 -0.715
. GroupKIV:MeasurementpreLaser 0.331 -0.234 -0.517 -0.646 0.462
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.1969648 -0.5906758 -0.1786371 0.4226713 7.2023893
.
. Number of Observations: 2034
. Number of Groups: 1291

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -3e-04 0e+00 -6.2317 0.0000 0.0000 -0.35 small
postLaser . KIT - KIV -5e-04 0e+00 -10.3603 0.0000 0.0000 -0.58 medium
postLaser . KIC - KIV -2e-04 0e+00 -4.7174 0.0000 0.0000 -0.26 small
preLaser . KIT - KIC -1e-04 1e-04 -1.2775 0.2018 0.4037 -0.09 very small
preLaser . KIT - KIV -2e-04 1e-04 -3.2009 0.0014 0.0057 -0.24 small
preLaser . KIC - KIV -1e-04 1e-04 -2.0684 0.0390 0.1169 -0.15 very small
. KIT postLaser - preLaser 0e+00 0e+00 -0.7288 0.4664 0.4664 -0.05 very small
. KIC postLaser - preLaser 2e-04 0e+00 3.8067 0.0002 0.0008 0.28 small
. KIV postLaser - preLaser 3e-04 1e-04 5.0681 0.0000 0.0000 0.37 small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 12 0.002495 43 0.001855 -6.289737 KIC04_12
KIT KIT03 preLaser 21 0.002094 34 0.000708 -7.253470 KIT03_21
KIV KIV12 postLaser 4 0.001797 31 0.000885 -7.029949 KIV12_4
KIT KIT05 postLaser 40 0.002731 52 0.001340 -6.614892 KIT05_40
KIT KIT09 postLaser 12 0.000842 49 0.000564 -7.480192 KIT09_12

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 4112.505 4157.424 -2048.253
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.3432709 0.5724252
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.346441 0.03083118 1288 -238.27958 0.0000
. GroupKIC 0.300289 0.04358016 1288 6.89051 0.0000
. GroupKIV 0.398199 0.04811049 1288 8.27677 0.0000
. MeasurementpreLaser 0.059279 0.04501488 740 1.31688 0.1883
. GroupKIC:MeasurementpreLaser -0.222429 0.06298672 740 -3.53136 0.0004
. GroupKIV:MeasurementpreLaser -0.201075 0.06967386 740 -2.88595 0.0040
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.707
. GroupKIV -0.641 0.453
. MeasurementpreLaser -0.510 0.361 0.327
. GroupKIC:MeasurementpreLaser 0.364 -0.515 -0.234 -0.715
. GroupKIV:MeasurementpreLaser 0.329 -0.233 -0.515 -0.646 0.462
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.4869293 -0.6075241 0.0596757 0.6371321 2.5760439
.
. Number of Observations: 2034
. Number of Groups: 1291

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.3003 0.0436 -6.8905 0.0000 0.0000 -0.38 small
postLaser . KIT - KIV -0.3982 0.0481 -8.2768 0.0000 0.0000 -0.46 small
postLaser . KIC - KIV -0.0979 0.0481 -2.0359 0.0420 0.1678 -0.11 very small
preLaser . KIT - KIC -0.0779 0.0551 -1.4118 0.1584 0.3169 -0.10 very small
preLaser . KIT - KIV -0.1971 0.0610 -3.2332 0.0013 0.0077 -0.24 small
preLaser . KIC - KIV -0.1193 0.0603 -1.9781 0.0483 0.1678 -0.15 very small
. KIT postLaser - preLaser -0.0593 0.0450 -1.3169 0.1883 0.3169 -0.10 very small
. KIC postLaser - preLaser 0.1631 0.0441 3.7032 0.0002 0.0016 0.27 small
. KIV postLaser - preLaser 0.1418 0.0532 2.6663 0.0078 0.0392 0.20 small
Note:
P value adjustment: holm method for 9 tests

VI Layer

RMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS
KIC KIC04 postLaser 9 0.002281 29 0.001260 -6.676414
KIV KIV09 postLaser 18 0.001057 31 0.000936 -6.974179
KIT KIT05 postLaser 24 0.001240 78 0.000487 -7.627878
KIT KIT08 preLaser 9 0.000349 7 0.000201 -8.510304
KIT KIT08 preLaser 24 0.000625 43 0.000328 -8.023737

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. -26252.92 -26207.73 13134.46
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.0002631663 0.0003848321
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) 0.0006717338 2.105691e-05 1320 31.90087 0.0000
. GroupKIC 0.0001238351 2.989757e-05 1320 4.14198 0.0000
. GroupKIV 0.0001495095 3.286683e-05 1320 4.54895 0.0000
. MeasurementpreLaser 0.0000092568 2.964100e-05 777 0.31230 0.7549
. GroupKIC:MeasurementpreLaser -0.0001205775 4.190596e-05 777 -2.87734 0.0041
. GroupKIV:MeasurementpreLaser -0.0000296328 4.617273e-05 777 -0.64178 0.5212
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.704
. GroupKIV -0.641 0.451
. MeasurementpreLaser -0.485 0.342 0.311
. GroupKIC:MeasurementpreLaser 0.343 -0.489 -0.220 -0.707
. GroupKIV:MeasurementpreLaser 0.312 -0.219 -0.487 -0.642 0.454
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -1.8637650 -0.5752573 -0.1839607 0.3440418 7.4463115
.
. Number of Observations: 2103
. Number of Groups: 1323

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -1e-04 0 -4.1420 0.0000 0.0003 -0.23 small
postLaser . KIT - KIV -1e-04 0 -4.5489 0.0000 0.0001 -0.25 small
postLaser . KIC - KIV 0e+00 0 -0.7786 0.4363 1.0000 -0.04 very small
preLaser . KIT - KIC 0e+00 0 -0.0863 0.9313 1.0000 -0.01 very small
preLaser . KIT - KIV -1e-04 0 -2.8796 0.0041 0.0245 -0.21 small
preLaser . KIC - KIV -1e-04 0 -2.8065 0.0051 0.0257 -0.20 small
. KIT postLaser - preLaser 0e+00 0 -0.3123 0.7549 1.0000 -0.02 very small
. KIC postLaser - preLaser 1e-04 0 3.7579 0.0002 0.0013 0.27 small
. KIV postLaser - preLaser 0e+00 0 0.5756 0.5651 1.0000 0.04 very small
Note:
P value adjustment: holm method for 9 tests

logRMS

Data overview
Sample of the data
Group Animal Measurement TrialNumber PeakAmp PeakLat RMS logRMS AnimalTrial
KIC KIC04 postLaser 9 0.002281 29 0.001260 -6.676414 KIC04_9
KIV KIV09 postLaser 18 0.001057 31 0.000936 -6.974179 KIV09_18
KIT KIT05 postLaser 24 0.001240 78 0.000487 -7.627878 KIT05_24
KIT KIT08 preLaser 9 0.000349 7 0.000201 -8.510304 KIT08_9
KIT KIT08 preLaser 24 0.000625 43 0.000328 -8.023737 KIT08_24

LMM

. Linear mixed-effects model fit by REML
. Data: model_data
. AIC BIC logLik
. 3688.364 3733.55 -1836.182
.
. Random effects:
. Formula: ~1 | AnimalTrial
. (Intercept) Residual
. StdDev: 0.3199188 0.490991
.
. Fixed effects: as.formula(paste0(metric, "~ Group*Measurement"))
. Value Std.Error DF t-value p-value
. (Intercept) -7.478471 0.02646895 1320 -282.53754 0.0000
. GroupKIC 0.156645 0.03758257 1320 4.16801 0.0000
. GroupKIV 0.204808 0.04131497 1320 4.95724 0.0000
. MeasurementpreLaser -0.010594 0.03772335 777 -0.28084 0.7789
. GroupKIC:MeasurementpreLaser -0.118148 0.05333310 777 -2.21528 0.0270
. GroupKIV:MeasurementpreLaser 0.039620 0.05876212 777 0.67425 0.5004
. Correlation:
. (Intr) GrpKIC GrpKIV MsrmnL GKIC:M
. GroupKIC -0.704
. GroupKIV -0.641 0.451
. MeasurementpreLaser -0.494 0.348 0.316
. GroupKIC:MeasurementpreLaser 0.349 -0.497 -0.224 -0.707
. GroupKIV:MeasurementpreLaser 0.317 -0.223 -0.496 -0.642 0.454
.
. Standardized Within-Group Residuals:
. Min Q1 Med Q3 Max
. -2.5914275 -0.5909434 0.0324091 0.5794265 2.9754833
.
. Number of Observations: 2103
. Number of Groups: 1323

Residuals check

Effects

Post-hoc tests
Multiple Comparisons
Measurement Group contrast estimate SE t.ratio p.value p.value.adj d eff_size
postLaser . KIT - KIC -0.1566 0.0376 -4.1680 0.0000 0.0002 -0.23 small
postLaser . KIT - KIV -0.2048 0.0413 -4.9572 0.0000 0.0000 -0.27 small
postLaser . KIC - KIV -0.0482 0.0415 -1.1619 0.2455 0.9819 -0.06 very small
preLaser . KIT - KIC -0.0385 0.0476 -0.8090 0.4188 1.0000 -0.06 very small
preLaser . KIT - KIV -0.2444 0.0525 -4.6587 0.0000 0.0000 -0.33 small
preLaser . KIC - KIV -0.2059 0.0524 -3.9322 0.0001 0.0006 -0.28 small
. KIT postLaser - preLaser 0.0106 0.0377 0.2808 0.7789 1.0000 0.02 very small
. KIC postLaser - preLaser 0.1287 0.0377 3.4148 0.0007 0.0034 0.25 small
. KIV postLaser - preLaser -0.0290 0.0451 -0.6442 0.5196 1.0000 -0.05 very small
Note:
P value adjustment: holm method for 9 tests 
# model_data <- model_data %>% 
#   mutate(TrialBinAnimal = paste(Animal, TrialBin, sep = "_"))
# 
# model_data$TrialBinAnimal <- factor(model_data$TrialBinAnimal)
# model_data$TrialBin <- factor(model_data$TrialBin)
# model_data$Animal <- factor(model_data$Animal)
# model_test <- lme(
#         fixed = as.formula(paste0(metric, "~ Group*Measurement")),
#         random=list(~1|Animal, ~1|TrialNumber),
#         data = model_data)
# 
# summary(model_test)
# bin_size <- 5
# # max_trial <- max(all_data$TrialNumber)
# 
# max_trial <- 49
# matrix(1:max_trial, nrow = max_trial/bin_size, byrow = TRUE)
model_data %>% 
  filter(Group == "KIC") %>% 
  ggboxplot(
    x = "Animal", y = "RMS",
    color = "Measurement", palette = "lancet", 
    add = "jitter",
    main = paste0(metric, " ~ Group | Measurement")
  )